The present study analyzed the bioactivity of whole body extracts from six solitary and eight colonial ascidian taxa against 20 sympatric bacterial isolates and one sympatric diatom species from the Western Antarctic Peninsula. Ascidians had crude lipophilic and hydrophilic extracts assayed against 20 bacterial strains. The lipophilic extract of one ascidian caused growth inhibition in all bacterial isolates at 3× tissue-level concentrations. The lipophilic and hydrophilic extracts were fractionated into seawater-soluble and insoluble fractions and assayed at three concentrations against a sympatric diatom species. Significant diatom mortality was detected at 3× and 1× concentrations in all but one ascidian taxon. Lipophilic fractions caused higher diatom mortality than hydrophilic extracts. The specificity of secondary metabolites against diatom fouling and the lack of activity against bacteria suggest high selective pressure for chemical defenses against diatom fouling or the potential that bacterial pathogens are controlled by the ascidian immune system.